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Science is increasingly pointing to a healthy gut in a baby being key for development of long term immunity, brain development and even emotional health. However, did you know that the key for this starts with your own gut? We take a look at the latest science around this and most crucially what you can do to give your baby the best start.

When it comes to optimising the health of you and your baby – your gut is where it’s at.

The link between your gut and your brain isn’t exactly new, it’s all something we’re aware of, even if just on a subconscious level. I mean in really simple terms, we all know that churning in our stomachs when we have anxiety or are nervous. But, did you realise that the health of your gut can potentially impact your baby’s own development?

Over the last decade or so, we have gained a much more profound understanding of just HOW fundamental and far reaching the gut and the microorganisms within it (microbiota) are. Ranging from influencing our emotions (anxiety and depression) to our immunity, our brain functionality and our hormonal balance.

Most crucially, however – research has suggested that it has an impact on how a baby’s brain develops and how its immune system functions and develops.

Sounds a bit far out? Well read on…

Whilst the research in this area has exploded (particularly over the last five to ten years), it is certainly fair to say that it is still developing and we do not fully understand all of the implications yet. What is pretty much certain, however, is that this is a topic that will become much better understood and more mainstream over the next decade or so.

So, if you haven’t heard much about it yet… you soon will…..

This extract from the Journal of Neuroscience sums it up pretty nicely:

‘The initial scepticism about reports suggesting a profound role of an intact gut microbiota in shaping brain neurochemistry and emotional behaviour has given way to an unprecedented paradigm shift in the conceptualisation of many psychiatric and neurological diseases….initial studies in humans seem to support the notion that there is a relationship between the complex world of the microbiota in our intestines and brain structure and function’. (1)

Translation: we do not understand it all yet, but it is becoming clearer that brain formation and a lot of modern day disease (particularly those that have been rapidly on the rise such as mental health based diseases like anxiety and depression/ADHD/Autism as well as obesity, diabetes and autoimmune conditions) appear to be linked to the health of our guts.

Pretty big stuff. So – here are a few things to get to grips with:

  • What exactly is the gut-brain axis?
  • How can this affect a developing baby?
  • What happens when this gets knocked off balance? (ie. when it goes wrong)
  • What we can do to get it in to the best shape possible?


This is a term that you will likely hear more and more, but it’s important to really understand WHY it can play such a significant role, particularly when it comes to health. Essentially it refers to the pretty complex bidirectional signalling that occurs between the brain and the gut, i.e. it’s not just a one way street – your gut is also influencing your brain just as your brain influences and controls the gut.

This is a huge topic, but, one aspect that I think sums up the relationship well is the fact that over 90% of our ‘happy hormone’ Serotonin (which is a crucial neurotransmitter) is actually produced by the gut. You may have heard of Serotonin, as it is used in certain antidepressant medications. That gives you an idea of its potency and impact.

We also know that when things pass through the gut that shouldn’t (when the lining is impaired, commonly known as ‘leaky gut’), that’s when you get autoimmune reactions, inflammation and other generalised health problems. If you take a step back it makes sense. The gut and your skin are the gateways between the outside world and your body – when these are impaired we have problems.

This snippet from a recent paper published in the Journal of Clinical Psychopharmacology and Neuroscience really emphasises how powerful what happens in your gut can be and some of the potential consequences if it goes wrong:

‘Based on evidence, the gut microbiota is associated with metabolic disorders such as obesity, diabetes mellitus and neuropsychiatric disorders such as schizophrenia, autistic disorders, anxiety disorders and major depressive disorders’. (2)

How is it so powerful?

Many of us don’t think too much about our guts, other than they digest our food. A few points to put how powerful it is into context:

  • There are ten times the number of microorganisms in the gut than the number of cells in the entire human body (known as the gut microbiota)
  • These microorganisms contain 150 x more genes than the human genome
  • The gut contains 1kg of bacteria (now that’s 1kg you dont want to lose!)

In fact, it is being increasingly referred to as the ‘second brain’ of the body, with the gut having been shown to produce key neuroactive compounds such as Serotonin of cours,e but also hunger related hormones ie. leptin and ghrelin.

In a nutshell it’s not something to be underestimated!

What do we mean by ‘gut health’?

Well on a very basic level, this relates to how well your gut does its job (filtering what goes in to our body). Once again, at this point science has no absolute answer (yet) as to what is the ‘perfect mix’ of bacteria to have in your gut – it is also person dependent. However, one thing we do know is that having a balanced (ie. where one microorganism isn’t overly dominant or overly lacking) and a good level of diversity is key.

So how does your gut health impact your baby’s development?

It starts with the baby’s very own gut microbiome which initially he or she will get from you. We know that colonization of the baby’s microbiome occurs as the baby is born (down the birth canal), from contact on the mother’s skin and from breastfeeding. However, there is something which we have only learnt more recently that takes it up a notch….

We have now discovered that a baby’s own gut microbiota gets built and established much earlier than we had originally thought. Previous understanding was the in utero environment was sterile (ie. no bacteria within the amniotic sac where they baby grows) which is now increasingly being disproved – VERY important if you’re thinking about giving a baby the best possible start:

‘As demonstrated in recent studies, the placenta and the amniotic fluid are not sterile… the microbiome in the first meconium of mice is not sterile, indicating that the microbiome colonozies the infant gut prior to parturition.’

Translation: a baby’s own microbiome starts building PRIOR to birth, so once again the state your own body is in prior and during pregnancy is crucial.

How is a baby’s own gut built?

Initailly it’s via you. The first bacteria that will colonise your baby’s gut is that which is picked up as the baby goes down the birth canal and from your skin during delivery and of course from what the baby eats – ideally from you once again.

Further, what is laid down at these very early stages is increasingly looking persistent and long lasting. In a review paper in the Journal of Clinical Psychopharmacology and Neuroscience Evrensel and Ceylon state that:

‘Clinical observations and animal trials have revealed much evidence of a strong link between the gut and the brain, which is established during the intrauterine period and the influence of which continues through the life of an individual.’

What is the intrauterine period? This is the period from conception to birth.

Okay, we now we understand how early it is established, how does it affect development?

There is some very interesting research showing that the gut plays a role in brain development and plasticity. What is neuroplasticity? This is the ability of the brain to change throughout an individual’s life. In a paper for Frontiers in Cellular Neuroscience published last year: Li, Han et al talked about how significant the influence of the gut has – particularly the brain and its development:

‘The gut microbiota influences brain development and behaviours through the neuroendocrine, neuroimmune and autonomic nervous systems’ (3)

In case you’re still not convinced. Mayer et al, in their paper, ‘Gut Microbes and the Brain: Paradigm Shift in Neuroscience’ state that:

‘overall, accumulating evidence in rodent studies suggests that there are links among the microbiota composition, brain biochemistry, and have our and that there interactions may be particularly important at critical neurodevelopmental windows’ (4)

It is also fundamental for a baby developing its own immunity.  They go on to cite an article published in Science showing the lifelong impact that this can have:

‘According to an article published in Science, microbiota diversity that develops during the perinatal period (ie. 22weeks from conception to seven days post birth) can have a lifelong effect on natural Killer T lymphocytes’

What are natural Killer T lymphocytes? They are part of your immune defence system – we really need those.

Further, more recent research has pointed to fibre consumption during pregnancy (prebiotic fibre in particular) potentially reducing the chances of a baby developing an increasingly common autoimmune condition: Celiac Disease.

Bottom line: we do not understand everything yet, much more research needs to be done. However, what seems fair to say is that if you really want to give your baby the best possible start in life, making sure your gut health is in optimal shape is a smart strategy.

So the next question is: How can we do this?

Well – a few things are known to throw the balance of your gut off – a lot of course being the classic issues of ‘modern’ life. Click here for more on this:

  • Stress (physical and mental)
  • Heavy antibiotic use
  • Processed Foods
  • Restricted and unbalanced diet (particularly one very high in sugar)
  • Over consumption of alcohol and caffeine

What can you do to improve your gut?

Well – quite a lot. Look up prebiotics, probiotics (are they worth your money?) and ‘feeding your belly’ . If you really want to geek it up – check out short chain fatty acids. Bottom line: the science is still evolving, but, this is a seriously exciting area and we do know that some tools easily at our disposal can be helpful and effective so no reason not to get started. No downside from having a healthy and balanced gut!




  1. MAYER E, KNIGHT R, MAZMANIAN S, CRYAN J, TILLISCH K: Gut Microbes and the Brain: Paradigm Shift in Neuroscience: The Journal of Neuroscience. 2012. November 2014 34(46) 15490-15496
  2. EVRENSEL A, CEYLAN, ME: The Gut-Brain Axis: The Missing Link in Depression: Clinical Psychopharmacology and Neuroscience: 2015; 13 (3): 239-244
  3. Li QINRUI, DY ABC, HAGERMAN J: The Gut Microbiota and Autism Spectrum Disorders: Frontiers in Cellular Neuroscience. 2017
  4. MAYER E, KNIGHT R, MAZMANIAN S, CRYAN J, TILLISCH K: Gut Microbes and the Brain: Paradigm Shift in Neuroscience: The Journal of Neuroscience. 2012. November 2014 34(46) 15490-15496


This article is for informational purposes only. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice. The information on this website has been developed following years of personal research and from referenced and sourced medical research. Before making any changes we strongly recommend you consult a healthcare professional before you begin.